If we had a hypotheical gene called gene exampleGene and this gene had 5 exons, labeled A, B, C, D, and E in that order on the chromosome, could it be the case that the stop codon for this gene be on exon D and the exon E still being a exon that would be transcribed in? I can not see this to be true, since If I remember correctly, transcription stops BEFORE the stop codon, and when stopped, the pre-mRNA is then further processed, but everything after that stop would not be a part of the exampleGene ?

2 Answers
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The coding region (ie the part that is translated) is between the start and stop codons, but the 5' and 3' untranslated regions (UTRs) are also transcribed by RNA polymerase; these are part of the first and last exons, respectively. The transcription start site is labelled right in front of the 5' UTR. For the purpose of this answer, transcription termination can be said to occur at the poly(A) signal (the poly(A) tail is added post-transcriptionally, as is the 5' cap).

To be clear, the point I'm hopefully making is that transcription does not involve codons. RNA polymerase does not stop at the stop codon nor does it start at the start codon. In fact, it doesn't even "know" what codons are.

$\begingroup$Thank you, this makes alot more sense now, but when you say RNA polymerase does not "stop at the stop codon" , could you detail that more? What I do not get is how RNA polymerase is initiated then. From what i remember various protein complexes initiate it, and then I assume various protein complexes end it.$\endgroup$
– Ro SivApr 26 '15 at 17:09

$\begingroup$@RoSiv In eukaryotes, the mechanism behind transcription termination is somewhat unclear. After the poly(A) sequence (AAUAAA) is transcribed, proteins recognize it and cleave the mRNA, after which it is polyadenylated. However, RNA polymerase continues to transcribe past the signal sequence. It is thought that, after cleavage, either RNAP is modified to become less processive and eventually falls off or an exonuclease begins degrading the second RNA until it catches up to RNAP and pulls the transcript out.$\endgroup$
– canadianerApr 26 '15 at 19:14

You mix up translation and transcription. Transcription creates mRNA from DNA template. Transcription also includes splicing, that is excision of introns so that mature mRNA contains only exons. In your example it goes like that:

DNA (chromosome): ---A----B--...--Dstop---E---

premature mRNA: A----B---...---Dstop--E---polyA

mature mRNA: AB..DstopE-polyA

Translation is the creation of polypeptide from template mature mRNA.

If codons in exon A correspond to polypeptide sequence a and so on for other exons, your polypeptide translated from mature mRNA will look something like that:

$NH_2$-ab..d-$COOH$

Stop codon stops translation. mRNA might still contain a lot of information after the stop codon, for example, for targeting mRNA to compartment of the cell (e.g. presynaptic site).

$\begingroup$@anndreev Yea i made a typo but will leave it in so your post is in context, thank you. But What I dont understand is for the E exon, how is that transcribed? Is that not the role of RNA polyemerase, to transcribe until it hits the point before a stop codon? How then, would that E be included into the premature mRNA, when it would be past the stop codon? And also, my chemistry is poor, but the NH2 would be the amino group, and the COOH the carboxyl group, which generlizes the form of a long polypeptide chain right?$\endgroup$
– Ro SivApr 26 '15 at 3:48

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$\begingroup$1) proteins are produces by ribosome from N to C end (yes, one is amino-, other is carboxyl-terminus); 2) RNA polymerase stops at the terminator sequence, it has nothing to do with codons, some RNAs are not even coding a protein! 3) Since exon E is before terminator, it will be processed via RNA polymerase. As I said, RNA after stop codon might be very useful for e.g. localization$\endgroup$
– aaaaaaApr 26 '15 at 4:23